# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 18:38:43 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: (3S)-3-[(2S)-2-amino-4-hydroxy-3-oxobutyl]pyrrolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C[C@@H]1CCNC1=O)C(=O)CO
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 OCQ  OCQ  (3S)-3-[(2S)-2-amino-4-hydroxy-3-oxobutyl]pyrrolidin-2-one  ligand  27  13  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_OCQ
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 OCQ  OAD   O  O     0  -0.495   2.5259  -0.6565  -1.9945
 OCQ  CD2   C  C     0   0.572   2.5306  -0.1599  -0.8795
 OCQ  NAH   N  NH1   0  -0.629   3.5078   0.5916  -0.3490
 OCQ  CAE   C  CH2   0  -0.258   3.2830   0.9937   1.0232
 OCQ  CD1   C  CH2   0  -0.470   1.7717   0.8096   1.1722
 OCQ  CG    C  CH1   0  -0.423   1.4350  -0.2942   0.1684
 OCQ  CB    C  CH2   0  -0.437   0.0389  -0.2297  -0.4295
 OCQ  CA    C  CH1   0  -0.227  -1.0600  -0.3578   0.6430
 OCQ  N     N  NH2   0  -0.785  -1.0451  -1.5908   1.4038
 OCQ  C     C  C     0   0.386  -2.4032  -0.2080  -0.0485
 OCQ  O     O  O     0  -0.391  -2.9701  -1.1470  -0.5518
 OCQ  CMK   C  CH2   0  -0.256  -2.9604   1.1880  -0.0731
 OCQ  OMP   O  OH1   0  -0.657  -4.0867   1.2472  -0.8915
 OCQ  HMP   H  HOH1  0   0.463  -4.4188   2.1492  -0.8750
 OCQ  HMK1  H  HCH2  0   0.245  -3.1733   1.4507   0.9751
 OCQ  HMK2  H  HCH2  0   0.233  -2.1583   1.8722  -0.3878
 OCQ  HA    H  HCH1  0   0.265  -0.9469   0.4723   1.3490
 OCQ  HN1   H  HNH2  0   0.347  -1.0513  -2.3876   0.7784
 OCQ  HN2   H  HNH2  0   0.357  -0.1878  -1.6544   1.9375
 OCQ  HB1   H  HCH2  0   0.240  -0.0743   0.7178  -0.9667
 OCQ  HB2   H  HCH2  0   0.251  -0.0852  -1.0291  -1.1648
 OCQ  HG    H  HCH1  0   0.276   1.5846  -1.2780   0.6331
 OCQ  HAH   H  HNH1  0   0.397   4.3913   0.7276  -0.8156
 OCQ  HAE1  H  HCH2  0   0.237   3.8376   0.3568   1.7181
 OCQ  HAE2  H  HCH2  0   0.252   3.5980   2.0234   1.1880
 OCQ  HD11  H  HCH2  0   0.258   1.4898   0.5705   2.1963
 OCQ  HD12  H  HCH2  0   0.247   1.2575   1.7322   0.8906

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 OCQ  OAD  CD2   double  1.221  0.020  1.221
 OCQ  CD2  CG    single  1.522  0.020  1.522
 OCQ  CD2  NAH   single  1.342  0.020  1.342
 OCQ  NAH  HAH   single  0.860  0.020  1.020
 OCQ  NAH  CAE   single  1.447  0.020  1.447
 OCQ  CAE  HAE1  single  0.970  0.020  1.090
 OCQ  CAE  HAE2  single  0.970  0.020  1.090
 OCQ  CAE  CD1   single  1.530  0.020  1.530
 OCQ  CD1  CG    single  1.530  0.020  1.530
 OCQ  CD1  HD11  single  0.970  0.020  1.090
 OCQ  CD1  HD12  single  0.970  0.020  1.090
 OCQ  CG   CB    single  1.520  0.020  1.520
 OCQ  CG   HG    single  0.970  0.020  1.090
 OCQ  CB   CA    single  1.541  0.020  1.541
 OCQ  CB   HB1   single  0.970  0.020  1.090
 OCQ  CB   HB2   single  0.970  0.020  1.090
 OCQ  CA   C     single  1.518  0.020  1.518
 OCQ  CA   HA    single  0.970  0.020  1.090
 OCQ  CA   N     single  1.449  0.020  1.449
 OCQ  N    HN1   single  0.890  0.020  1.040
 OCQ  N    HN2   single  0.890  0.020  1.040
 OCQ  C    CMK   single  1.503  0.020  1.503
 OCQ  C    O     double  1.207  0.020  1.207
 OCQ  CMK  OMP   single  1.394  0.020  1.394
 OCQ  CMK  HMK1  single  0.970  0.020  1.090
 OCQ  CMK  HMK2  single  0.970  0.020  1.090
 OCQ  OMP  HMP   single  0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 OCQ  CG    CD2  NAH   107.54  3.000
 OCQ  NAH   CD2  OAD   126.28  3.000
 OCQ  CG    CD2  OAD   126.18  3.000
 OCQ  HAH   NAH  CAE   122.50  3.000
 OCQ  CAE   NAH  CD2   114.66  3.000
 OCQ  HAH   NAH  CD2   122.04  3.000
 OCQ  HAE2  CAE  HAE1  107.92  3.000
 OCQ  HAE2  CAE  CD1   112.62  3.000
 OCQ  HAE1  CAE  CD1   111.65  3.000
 OCQ  CD1   CAE  NAH   102.26  3.000
 OCQ  HAE2  CAE  NAH   111.17  3.000
 OCQ  HAE1  CAE  NAH   111.21  3.000
 OCQ  HD12  CD1  HD11  107.81  3.000
 OCQ  HD12  CD1  CG    109.66  3.000
 OCQ  HD11  CD1  CG    113.69  3.000
 OCQ  HD12  CD1  CAE   109.76  3.000
 OCQ  HD11  CD1  CAE   111.95  3.000
 OCQ  CG    CD1  CAE   103.91  3.000
 OCQ  HG    CG   CB    109.24  3.000
 OCQ  HG    CG   CD1   109.80  3.000
 OCQ  CB    CG   CD1   115.45  3.000
 OCQ  HG    CG   CD2   105.80  3.000
 OCQ  CB    CG   CD2   112.74  3.000
 OCQ  CD1   CG   CD2   103.28  3.000
 OCQ  HB2   CB   HB1   106.92  3.000
 OCQ  HB2   CB   CA    109.05  3.000
 OCQ  HB1   CB   CA    109.86  3.000
 OCQ  HB2   CB   CG    109.74  3.000
 OCQ  HB1   CB   CG    108.94  3.000
 OCQ  CA    CB   CG    112.19  3.000
 OCQ  HA    CA   C     108.06  3.000
 OCQ  HA    CA   N     107.78  3.000
 OCQ  C     CA   N     109.41  3.000
 OCQ  N     CA   CB    115.40  3.000
 OCQ  HA    CA   CB    108.18  3.000
 OCQ  C     CA   CB    107.80  3.000
 OCQ  HN2   N    HN1   106.34  3.000
 OCQ  HN2   N    CA    109.82  3.000
 OCQ  HN1   N    CA    110.19  3.000
 OCQ  CMK   C    O     122.79  3.000
 OCQ  O     C    CA    121.93  3.000
 OCQ  CMK   C    CA    115.28  3.000
 OCQ  HMK2  CMK  HMK1  105.36  3.000
 OCQ  HMK2  CMK  OMP   113.25  3.000
 OCQ  HMK1  CMK  OMP   113.11  3.000
 OCQ  HMK2  CMK  C     108.18  3.000
 OCQ  HMK1  CMK  C     106.12  3.000
 OCQ  OMP   CMK  C     110.41  3.000
 OCQ  HMP   OMP  CMK   108.00  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 OCQ  CONST_01  CG   CD2  NAH  CAE    0.00   0.0  0
 OCQ  CONST_02  CAE  NAH  CD2  OAD  180.00   0.0  0
 OCQ  CONST_03  HAH  NAH  CD2  CG   180.00   0.0  0
 OCQ  Var_01    CD1  CAE  NAH  CD2  -19.56  30.0  1
 OCQ  Var_02    CG   CD1  CAE  NAH   27.74  30.0  1
 OCQ  Var_03    OMP  CMK  C    CA   171.38  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 OCQ  chir_01  CG  CD2  CD1  CB  negativ
 OCQ  chir_02  CA  N    C    CB  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 OCQ  plan-1  CA   0.020
 OCQ  plan-1  C    0.020
 OCQ  plan-1  O    0.020
 OCQ  plan-1  CMK  0.020
 OCQ  plan-2  OAD  0.020
 OCQ  plan-2  CD2  0.020
 OCQ  plan-2  NAH  0.020
 OCQ  plan-2  CAE  0.020
 OCQ  plan-2  CG   0.020
 OCQ  plan-2  HAH  0.020

